Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate 7023042 Shewana3_0280 ABC transporter related (RefSeq)
Query= TCDB::P31134 (377 letters) >FitnessBrowser__ANA3:7023042 Length = 367 Score = 166 bits (420), Expect = 1e-45 Identities = 92/230 (40%), Positives = 140/230 (60%), Gaps = 10/230 (4%) Query: 45 GEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML------DGVDLSQVPPYLRPINMMFQ 98 GE+ A++G SG GK+TLLRM+AG P AG I+ D + + P R I M Q Sbjct: 29 GEVLAVVGPSGGGKTTLLRMIAGLNHPDAGSIVFGETLWFDHQSRTALTPQQRHIGYMPQ 88 Query: 99 SYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRV 158 + LFP++T +N+ GL D +PK+E +R + L V++ R P LSGGQRQRV Sbjct: 89 HFGLFPNLTALENVVAGL--DHIPKSERIARAKDWLERVNLHGLPDRLPMHLSGGQRQRV 146 Query: 159 ALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAG 218 ALAR+LA+ P +LLLDEP A+D++ R+R+ LE+ + E++ +MVTHD EA+ +A Sbjct: 147 ALARALAREPSVLLLDEPFSAVDRETRERLYLELARLKEQLLCPVIMVTHDLNEALLLAD 206 Query: 219 RIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFEG--VLKERQED 266 + ++++G+ +Q G P E+ P A +G N+F+G V ++R +D Sbjct: 207 SMILISQGQMLQQGAPFEVLSRPRNEAVARQMGLRNIFDGEVVFQDRTKD 256 Lambda K H 0.321 0.137 0.400 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 286 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 377 Length of database: 367 Length adjustment: 30 Effective length of query: 347 Effective length of database: 337 Effective search space: 116939 Effective search space used: 116939 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory